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* gnu: r-digest: Update to 0.6.12.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/statistics.scm (r-digest): Update to 0.6.12.
* gnu: r-survival: Update to 2.41-3.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/statistics.scm (r-survival): Update to 2.41-3.
* gnu: r-mgcv: Update to 1.8-17.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/statistics.scm (r-mgcv): Update to 1.8-17.
* gnu: r-matrix: Update to 1.2-8.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/statistics.scm (r-matrix): Update to 1.2-8.
* gnu: r-lattice: Update to 0.20-35.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/statistics.scm (r-lattice): Update to 0.20-35.
* gnu: r-rprojroot: Update to 1.2.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/statistics.scm (r-rprojroot): Update to 1.2.
* gnu: r-htmltable: Update to 1.9.Ricardo Wurmus2017-04-06
| | | | | * gnu/packages/web.scm (r-htmltable): Update to 1.9. [propagated-inputs]: Add "r-checkmate" and "r-htmlwidgets".
* gnu: r-curl: Update to 2.4.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/web.scm (r-curl): Update to 2.4.
* gnu: r-genomeinfodb: Update to 1.10.3.Ricardo Wurmus2017-04-06
| | | | | * gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.10.3. [propagated-inputs]: Add "r-rcurl".
* gnu: r-xvector: Update to 0.14.1.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/bioinformatics.scm (r-xvector): Update to 0.14.1.
* gnu: r-bioccheck: Update to 1.10.1.Ricardo Wurmus2017-04-06
| | | | | * gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.10.1. [propagated-inputs]: Remove "r-knitr" and "r-devtools".
* gnu: r-tidyr: Update to 0.6.1.Ricardo Wurmus2017-04-06
| | | | | * gnu/packages/statistics.scm (r-tidyr): Update to 0.6.1. [propagated-inputs]: Add "r-tibble".
* gnu: r-roxygen2: Update to 6.0.1.Ricardo Wurmus2017-04-06
| | | | | * gnu/packages/statistics.scm (r-roxygen2): Update to 6.0.1. [propagated-inputs]: Add "r-commonmark", "r-desc", "r-r6", and "r-xml2".
* gnu: Add r-commonmark.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/statistics.scm (r-commonmark): New variable.
* gnu: Add r-desc.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/statistics.scm (r-desc): New variable.
* gnu: r-readr: Update to 1.1.0.Ricardo Wurmus2017-04-06
| | | | | * gnu/packages/statistics.scm (r-readr): Update to 1.1.0. [propagated-inputs]: Remove "r-curl".
* gnu: r-tibble: Update to 1.3.0.Ricardo Wurmus2017-04-06
| | | | | * gnu/packages/statistics.scm (r-tibble): Update to 1.3.0. [propagated-inputs]: Remove "r-assertthat".
* gnu: r-jsonlite: Update to 1.3.Ricardo Wurmus2017-04-06
| | | | * gnu/packages/web.scm (r-jsonlite): Update to 1.3.
* gnu: ldc-bootstrap: Delete failing test.Ricardo Wurmus2017-04-06
| | | | | * gnu/packages/ldc.scm (ldc-bootstrap)[arguments]: Delete failing test in build phase.
* gnu: guile-aspell: Switch to Guile 2.2.Ludovic Courtès2017-04-06
| | | | | * gnu/packages/guile.scm (guile-aspell)[inputs]: Replace GUILE-2.0 with GUILE-2.2.
* gnu: guile-aspell: Remove hard-coded "site/2.0" from $(guilesitedir).Ludovic Courtès2017-04-06
| | | | | * gnu/packages/guile.scm (guile-aspell)[arguments]: Remove #:configure-flags. Add 'set-guilesitedir' phase.
* gnu: guile-aspell: Update to 0.4.Ludovic Courtès2017-04-06
| | | | | | * gnu/packages/guile.scm (guile-aspell): Update to 0.4. [arguments] <#:phases>: Adjust 'set-libaspell-file-name' to new source tree layout.
* system: Support the --root option in 'guix system'.Chris Marusich2017-04-06
| | | | | | | | | | | | | Fixes <https://bugs.gnu.org/26271>. * guix/scripts/system.scm (perform-action): Add #:gc-root parameter and honor it. (show-help): Document the --root option. (%options): Add 'root'. (process-action): Pass 'root' option to perform-action as #:gc-root. * doc/guix.texi (Invoking guix system): Document '--root'. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* build: Add and export procedure 'register-root*'.Chris Marusich2017-04-06
| | | | | | * guix/scripts/build.scm (register-root*): Add and export it. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* environment: Deal with single-entry search paths.Ludovic Courtès2017-04-05
| | | | | | | This is a followup to fcd75bdbfa99d14363b905afbf914eec20e69df8. * guix/scripts/environment.scm (create-environment): Check whether SEPARATOR is #f.
* doc: Add "Documentation" section.Ludovic Courtès2017-04-05
| | | | * doc/guix.texi (Documentation): New node.
* profiles: Generate database file for man pages.Maxim Cournoyer2017-04-05
| | | | | | | | | | | The mandb database file (index.db) is used by the "apropos" (whatis) or "man -k" commands. This change introduces a profile hook to generate such database file. * guix/profiles.scm (manual-database): New procedure. (%default-profile-hooks): Add it. Co-authored-by: Ludovic Courtès <ludo@gnu.org>
* build-system/python: 'package-with-explicit-python' uses 'package-mapping'.Ludovic Courtès2017-04-05
| | | | | | | * guix/build-system/python.scm (package-with-explicit-python) [package-variant, cut?]: New procedures. [transform]: Remove 'mlambdaq' form and input tuple handling. Use 'package-mapping'.
* packages: Add 'package-mapping' and base 'package-input-rewriting' on it.Ludovic Courtès2017-04-05
| | | | | | | * guix/packages.scm (package-mapping): New procedure. (package-input-rewriting): Rewrite in terms of 'package-mapping'. * tests/packages.scm ("package-mapping"): New test. * doc/guix.texi (Defining Packages): Document it.
* Revert "gnu: openexr: Add IlmBase include sub-directory to 'OpenEXR.pc'."Ludovic Courtès2017-04-05
| | | | | | This reverts commit 01fe019166fe8a925b3bf3b489792b52b1b6ca7a, which was unneeded because IlmBase is already listed as 'Requires' in 'OpenEXR.pc'.
* Revert "gnu: bc: Update to 1.07."Tobias Geerinckx-Rice2017-04-05
| | | | | This reverts commit dfee7daedb760f1b1d7506829ca31633f4173356. It causes the linux-libre@4.9 build to hang (command-line usage works fine).
* gnu: Move audacity to audio.scm.Kei Kebreau2017-04-05
| | | | | | * gnu/packages/audacity.scm: Remove file and move audacity... * gnu/packages/audio.scm: ...here. * gnu/local.mk: Remove reference to removed file.
* import cran: Distinguish Bioconductor data packages.Ricardo Wurmus2017-04-05
| | | | | | * guix/import/cran.scm (bioconductor-package?): Exclude Bioconductor data packages. (bioconductor-data-package?): New procedure.
* gnu: sra-tools: Fix glibc naming conflict.Ricardo Wurmus2017-04-05
| | | | | * gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Add build phase "patch-away-glibc-conflict" to fix a definition conflict with glibc 2.25.
* gnu: sra-tools: Use "modify-phases" syntax.Ricardo Wurmus2017-04-05
| | | | | * gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Use "modify-phases" syntax.
* gnu: diamond: Update to 0.8.37.Ben Woodcroft2017-04-05
| | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.8.37.
* download: Update the GnuPG mirror list.Leo Famulari2017-04-05
| | | | * guix/download.scm (%mirrors) <gnupg>: Use HTTP for TU Wien mirror.
* gnu: kdevelop: Update to 5.1.0.Thomas Danckaert2017-04-05
| | | | * gnu/packages/kde.scm (kdevelop, kdevplatform): Update to 5.1.0.
* gnu: bc: Update to 1.07.Tobias Geerinckx-Rice2017-04-05
| | | | | | * gnu/packages/algebra.scm (bc): Update to 1.07. [native-inputs]: Add ed and texinfo. [arguments]: Use default ‘configure’ phase.
* gnu: bc: Actually use readline.Tobias Geerinckx-Rice2017-04-05
| | | | | * gnu/packages/algebra.scm (bc)[arguments]: Add ‘--with-readline’ to #:configure-flags.
* gnu: algebra: Re-order imports.Tobias Geerinckx-Rice2017-04-05
| | | | * gnu/packages/algebra.scm: Order imports alphabetically.
* gnu: openexr: Add IlmBase include sub-directory to 'OpenEXR.pc'.Ludovic Courtès2017-04-05
| | | | | * gnu/packages/graphics.scm (openexr)[arguments]: Add 'set-ilmbase-directory-in-pc-file' phase.
* services: cuirass: Wait for networking.Ludovic Courtès2017-04-05
| | | | | * gnu/services/cuirass.scm (cuirass-shepherd-service): Add 'networking' to 'requirements'.
* build: Export register-root procedure.Chris Marusich2017-04-05
| | | | | | * guix/scripts/build.scm: Export register-root procedure. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: icecat: Use bundled ICU to avoid crashes.Clément Lassieur2017-04-04
| | | | | * gnu/packages/gnuzilla.scm (icecat)[arguments] <#:configure-flags>: Temporarily comment out "--with-system-icu".
* gnu: icecat: Re-enable parallel build.Clément Lassieur2017-04-04
| | | | * gnu/packages/gnuzilla.scm (icecat)[arguments]: Re-enable parallel build.
* gnu: python-django: Specify CPE name.Marius Bakke2017-04-04
| | | | | * gnu/packages/django.scm (python-django, python2-django)[properties]: Add "cpe-name".
* gnu: python-django: Update to 1.10.7 [fixes CVE-2017-7233 and CVE-2017-7234].Marius Bakke2017-04-04
| | | | * gnu/packages/django.scm (python-django, python2-django): Update to 1.10.7.
* gnu: gnupg: Update to 2.1.20.Marius Bakke2017-04-04
| | | | | | | * gnu/packages/gnupg.scm (gnupg): Update to 2.1.20. [source]: Remove patch. * gnu/packages/patches/gnupg-2.1-fix-Y2038-test-failure.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Remove it.
* gnu: python2-cython: Fix build on 32-bit platforms.Marius Bakke2017-04-04
| | | | | | * gnu/packages/python.scm (python-cython, python2-cython)[source]: Add patch. * gnu/packages/patches/python-cython-fix-tests-32bit.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it.
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